The flow of polarized light through a metal film with an array of microchannels is controlled by the phase of an optically active, phospholipid nanocoating, even though the coating does not cover the open area of the microchannels. The molecular details of the assembly (DPPC phospholipid monolayer/bilayer on a hexadecanethiol monolayer on a copper- or nickel-coated microarray) were determined using the infrared, surface-plasmon-mediated, extraordinary transmission of the metal microarrays. Infrared absorption spectra with greatly enhanced absorptions by comparison to literature were recorded and used as a diagnostic for the phase, composition, and molecular geometry of these nanocoatings. This approach presents new tools for nanoscale construction in constricted microspaces, which may ultimately be useful with individual microchannels.